Plant transcriptional memory and associated mechanism of abiotic stress tolerance

DNA methylation regulates somatic stress memory and mediates plasticity during acclimation to repeated sulfide stress in Urechis unicinctus

Stress memory is an adaptive mechanism that enables organisms to develop resilience in response to environmental changes. Among them, somatic stress memory is an important means for organisms to cope with contemporary repeated stress, and is accompanied by transcription memory. Sulfide is a common environmental pollutant; however, some organisms have adapted to survive in sulfur-rich environments. Urechis unicinctus is a sulfur-tolerant organism that enhances sulfide stress tolerance by establishing a somatic sulfide stress memory mechanism. However, the molecular mechanisms that regulate sulfide stress memory remain unclear. To explore whether epigenetics, which plays a role in the response of organisms to environmental stress, is involved in regulating somatic sulfide stress memory, we performed a combined analysis of DNA methylation and transcriptome data. We found that elevated levels of DNA methylation under repetitive sulfide stress regulated gene expression and resulted in enhanced sulfide stress tolerance in U. unicinctus, a phenomenon verified using DNA methylase inhibitors. Transcriptional memory can be induced in genes related to oxidative stress, regulation of autophagy, and maintenance of protein homeostasis by altering the level of DNA methylation to facilitate sulfide stress acclimation. Our results provide new insights into adaptive mechanisms to cope with environmental fluctuations.

Genome-Wide Analysis of CPP Transcription Factor Family in Endangered Plant Phoebe bournei and Its Response to Adversity

The CPP gene family comprises transcription factor genes containing a conserved CRC domain, which is mainly involved in plant development and evolution. Although CPP genes have been widely studied in many plants, little is known about them in woody plants, especially in the endangered species Phoebe bournei (Hemsl.). In the genome of Phoebe bournei, we identified 11 PbCPP genes (PbCPP1-PbCPP11) distributed on four chromosomes, with large differences in the number of amino acids. They encode both acidic and alkaline proteins. A phylogenetic analysis showed that these PbCPP genes can be divided into three subfamilies, A, B, and C, which contain seven, two, and two genes, respectively. Through an interspecific collinearity analysis, we identified homologous PbCPP genes. A promoter cis-acting element analysis revealed that PbCPPs contain a variety of elements that respond to plant hormones, stress signals, and light and play a role in growth and development, and most PbCPP genes (except PbCPP3 and PbCPP8) contain MYB binding site elements that regulate drought-induced stress responses, indicating that they play an important role in plant drought resistance. An expression analysis showed that PbCPP3 and PbCPP4 expression was high in the roots and stems and lower in the leaves, whereas the expression of most of the other genes was low in the roots, stems, and leaves. In addition, six representative PbCPP genes were detected using qRT-PCR. The results show significant differences in the expression of PbCPP genes under abiotic stress conditions (drought, cold, and salt), indicating that they play an important role in stress responses. This study preliminarily verified the role of the PbCPP gene family in different abiotic stress responses, which is of great significance for understanding its mechanism in plant growth and development and stress adaptation.

Abiotic stress-induced changes in Tetrastigma hemsleyanum: insights from secondary metabolite biosynthesis and enhancement of plant defense mechanisms

Tetrastigma hemsleyanum, a traditional Chinese medicinal plant with anti-inflammatory, anti-cancer, and anti-tumor properties, faces increasing abiotic stress due to climate change, agricultural chemicals, and industrialization. This study investigated how three abiotic stress factors influence antioxidant enzyme activity, MDA levels, DPPH free radical scavenging capacity, chlorophyll, carotenoids, active compounds, and gene expression in different T. hemsleyanum strains. The comprehensive evaluation indicates that the ZJWZ strain holds potential as a preferred parental material for future resistance breeding. Furthermore, PAL gene expression was strongly positively correlated with flavonoid and phenol contents, highlighting its role in the stress response through the phenylpropanoid-flavonoid pathway. This study contributes to the standardization of the production and breeding of superior strains of T. hemsleyanum. It also lays the foundation for investigating how plants react to environmental stressors.

Hydrogen peroxide priming triggers splicing memory in grape berries

Plants are highly sensitive to environmental changes, and alternative splicing (AS) has been described in many studies due to its important control role in stress response. Recent studies indicated that plants exhibit splicing memory to stress to effectively activate transcriptional adaptation. Hydrogen peroxide (H2O2), as a reactive oxygen species (ROS), has toxic effects on plants. However, it also has a significant effect on promoting early maturity of 'Kyoho' grape at low concentrations. To explore the mechanism of priming treatment of H2O2 showing better promotion effect, the RNA-Seq data of H2O2-primied and no-primied fruits were analyzed. The genes with H2O2 stress splicing memory were identified, accompanied by changes in H3K4me3 modification levels, and their splicing memory patterns were verified by PCR and agarose gel electrophoresis. This finding establishes a link between alternative splicing memory and fruit ripening under H2O2 regulation and contribute to develop the application of H2O2 in fruit ripening.

Tree post-drought recovery: scenarios, regulatory mechanisms and ways to improve

Efficient post-drought recovery of growth and assimilation enables a plant to return to its undisturbed state and functioning. Unlike annual plants, trees suffer not only from the current drought, but also from cumulative impacts of consecutive water stresses which cause adverse legacy effects on survival and performance. This review provides an integrated assessment of ecological, physiological and molecular evidence on the recovery of growth and photosynthesis in trees, with a view to informing the breeding of trees with a better ability to recover from water stress. Suppression of recovery processes can result not only from stress damage but also from a controlled downshift of recovery as part of tree acclimation to water-limited conditions. In the latter case, recovery processes could potentially be activated by turning off the controlling mechanisms, but several obstacles make this unlikely. Tree phenology, and specifically photoperiodic constraints, can limit post-drought recovery of growth and photosynthesis, and targeting these constraints may represent a promising way to breed trees with an enhanced ability to recover post-drought. The mechanisms of photoperiod-dependent regulation of shoot, secondary and root growth and of assimilation processes are reviewed. Finally, the limitations and trade-offs of altering the photoperiodic regulation of growth and assimilation processes are discussed.

To live or let die? Epigenetic adaptations to climate change-a review

Anthropogenic activities are responsible for a wide array of environmental disturbances that threaten biodiversity. Climate change, encompassing temperature increases, ocean acidification, increased salinity, droughts, and floods caused by frequent extreme weather events, represents one of the most significant environmental alterations. These drastic challenges pose ecological constraints, with over a million species expected to disappear in the coming years. Therefore, organisms must adapt or face potential extinctions. Adaptations can occur not only through genetic changes but also through non-genetic mechanisms, which often confer faster acclimatization and wider variability ranges than their genetic counterparts. Among these non-genetic mechanisms are epigenetics defined as the study of molecules and mechanisms that can perpetuate alternative gene activity states in the context of the same DNA sequence. Epigenetics has received increased attention in the past decades, as epigenetic mechanisms are sensitive to a wide array of environmental cues, and epimutations spread faster through populations than genetic mutations. Epimutations can be neutral, deleterious, or adaptative and can be transmitted to subsequent generations, making them crucial factors in both long- and short-term responses to environmental fluctuations, such as climate change. In this review, we compile existing evidence of epigenetic involvement in acclimatization and adaptation to climate change and discuss derived perspectives and remaining challenges in the field of environmental epigenetics. Graphical Abstract.

A review of the potential involvement of small RNAs in transgenerational abiotic stress memory in plants

Crop production is increasingly threatened by the escalating weather events and rising temperatures associated with global climate change. Plants have evolved adaptive mechanisms, including stress memory, to cope with abiotic stresses such as heat, drought, and salinity. Stress memory involves priming, where plants remember prior stress exposures, providing enhanced responses to subsequent stress events. Stress memory can manifest as somatic, intergenerational, or transgenerational memory, persisting for different durations. The chromatin, a central regulator of gene expression, undergoes modifications like DNA acetylation, methylation, and histone variations in response to abiotic stress. Histone modifications, such as H3K4me3 and acetylation, play crucial roles in regulating gene expression. Abiotic stresses like drought and salinity are significant challenges to crop production, leading to yield reductions. Plant responses to stress involve strategies like escape, avoidance, and tolerance, each influencing growth stages differently. Soil salinity affects plant growth by disrupting water potential, causing ion toxicity, and inhibiting nutrient uptake. Understanding plant responses to these stresses requires insights into histone-mediated modifications, chromatin remodeling, and the role of small RNAs in stress memory. Histone-mediated modifications, including acetylation and methylation, contribute to epigenetic stress memory, influencing plant adaptation to environmental stressors. Chromatin remodeling play a crucial role in abiotic stress responses, affecting the expression of stress-related genes. Small RNAs; miRNAs and siRNAs, participate in stress memory pathways by guiding DNA methylation and histone modifications. The interplay of these epigenetic mechanisms helps plants adapt to recurring stress events and enhance their resilience. In conclusion, unraveling the epigenetic mechanisms in plant responses to abiotic stresses provides valuable insights for developing resilient agricultural techniques. Understanding how plants utilize stress memory, histone modifications, chromatin remodeling, and small RNAs is crucial for designing strategies to mitigate the impact of climate change on crop production and global food security.